ATAC-qPCR

To examine the control of Axud1E1 accessibility, we performed ATAC-qPCR in embryos transfected with a TFAP2A morpholino. HH4 embryos were bilaterally injected with control and targeted morpholinos, as described previously. Embryos were incubated at 37°C until HH9, when dorsal neural folds were surgically dissected. Paired single neural folds were individually processed for DNA tagmentation following the ATAC protocol described in [17]. For each genomic location, specific enrichment was quantified by RT-PCR (S5 Table). Raw CT values were first normalized to a control region defined by the absence of transcription factor binding, no enrichment of active histone marks and low DNA accessibility in our CUT&RUN and ATAC datasets. Changes in chromatin accessibility in morpholino treated samples were subsequently compared to control samples.